When the config was validated for siteB did it show types being matched? Because you defined the SiteCollection for your DataMapping I would assume a validation of siteB would show nothing though of course it would succeed in "validating".
When I have activated SLAM against site collections in a multi-sitecollection configuration I have not seen this occur where the wrong site collection data mapping is used. In this case I would suspect that you ran it against siteA instead of siteB.

As for the activation against the blank site, I assume you did not mean a blank site collection, what is the "phantom list"? You say you did not add any lists to the blank site. You activated SLAM but lists are configured from other
sites, and activation of SLAM occurs from the root of the site collection.